>>537794759
The gap between the Emperor protecting you and you using the hammer to free Orpheus and convincing him to protect you is a minute or a couple minutes at most. He probably did protect you during that time just to have the conversation, in which he decided whether or not he wanted to kill you.
Another thing to consider is that the brain's standing orders from the Chosen were not to turn the infected. They wanted people infected and controlled, but not turned yet because they were waiting to turn them all at once as part of a coup. The only evidence we have that the brain was going against these orders and trying to turn you is....the Emperor telling us that. So it's entirely possible that the brain wasn't actually actively trying to turn us, and the Emperor was lying in order to puff up how much he was actually doing for us. This would explain why we don't instantly turn during the seconds/minutes in between Emps and Orphy protecting us.
Another thing to consider is that the brain figures out who we are pretty early, they do it during act 2 when we visit Moonrise. It knows all about the prism and the prism bearers, but the brain actually helps us because it wants us to murder the Chosen and destabilize their control over the Crown. Our actions throughout the game were the manipulations of the brain at all times. So the brain actually probably wouldn't want to turn us in act 1 or act 2 while it still needed us to murder Gort and Orin.
This type of stuff is why the game is actually pretty well written, despite what people will sometimes say here. Most people who say that aren't even aware of any of this part, and you know that because they'll criticize the surface level plot without mentioning any of this which tells you they don't even know the actual plot of the game.